Preferences help
enabled [disable] Abstract
Number of results
2005 | 52 | 1 | 71-86
Article title

FEDMA - a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

Title variants
Languages of publication
A theoretical model of a chain of irreversible Michaelis-Menten reactions proceeding inside a living cell, taking cell growth, division and subcellular compartmentation into account, was proposed. It became a basis for the construction of a "fuzzy" enzymatic data-modeling algorithm (FEDMA) - a procedure allowing the estimation of missing parameter values for the modeled system, in accordance both with the derived theoretical rules and the available experimental data. The obtained tool was tested to model the heme biosynthesis pathway in Saccharomyces cerevisiae, where about 40% of parameters remain unknown. The missing parameters estimated by means of FEDMA fall in the range of expected values.
Physical description
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
  • Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD. (1983) Macromolecules: structure, shape, and information. In Molecular Biology of the Cell. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD, eds, pp 89-138. Garland Publishing Inc., New York.
  • Alwan AF, Mgbeje BIA, Jordan PM. (1989) Purification and properties of uroporphyrinogen III synthase (co-synthase) from an overproducing recombinant strain of Escherichia coli K-12. Biochem J.; 264: 397-402.
  • Borralho LM, Ortiz CHD, Panek AD, Mattoon JR. (1990) Purification of δ-aminolevulinate dehydratase from genetically engineered yeast. Yeast.; 6: 319-30.
  • Camadro JM, Chambon H, Jolles J, Labbe P. (1986) Purification and properties of coproporphyrinogen oxidase from the yeast Saccharomyces cerevisiae. Eur J Biochem.; 156: 579-87.
  • Camadro JM, Thome F, Brouillet N, Labbe P. (1994) Purification and properties of protoporphyrinogen oxidase from the yeast Saccharomyces cerevisiae. J Biol Chem.; 269: 32085-91.
  • Carvajal E, Panek AD, Mattoon JR. (1990) Isolation and characterization of a new mutant of Saccharomyces cerevisiae with altered synthesis of 5-aminolevulinic acid. J Bacteriol.; 172: 2855-61.
  • Correa Garcia SR, Rossett MV, Batlle AM. (1991) Studies on porphobilinogen deaminase from Saccharomyces cerevisiae. Z Naturforsch C.; 46: 1017-23.
  • Felix F, Brouillet N. (1990) Purification and properties of uroporphyrinogen decarboxylase from Saccharomyces cerevisiae. Eur J Biochem.; 188: 393-403.
  • Fumagalli SA, Kotler ML, Rossetti MV, Batlle AM. (1991) Studies on uroporphyrinogen biosynthesis in pig liver. Z Naturforsch C.; 46: 1101-8.
  • Goldbeter A. (1991) A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc Natl Acad Sci USA.; 88: 9107-11.
  • Hart GJ, Battersby AR. (1985) Purification and properties of uroporphyrinogen III synthase (co-synthetase) from Euglena gracilis. Biochem J.; 232: 151-60.
  • Hoffman M, Góra M, Rytka J. (2003) Identification of rate-limiting steps in yeast heme biosynthesis. Biochem Biophys Res Commun.; 310: 1247-53.
  • Jones RM, Jordan PM. (1993) Purification and properties of the uroporphyrinogen decarboxylase from Rhodobacter sphaeroides. Biochem J.; 293: 703-12.
  • Kurlandzka A, Żołądek T, Rytka J, Labbe-Bois R, Urban-Grimal D. (1988) The effects in vivo of mutationally modified uroporphyrinogen decarboxylase in different hem12 mutants of baker's yeast (Saccharomyces cerevisiae). Biochem J.; 253: 109-16.
  • Kuzmic P. (1996) Program DYNAFIT for the analysis of enzyme kinetic data. Application to HIV proteinase. Anal Biochem.; 237: 260-73.
  • Labbe-Bois R, Labbe P. (1990) Tetrapyrrole and heme biosynthesis in the yeast Saccharomyces cerevisiae. In Biosynthesis of Heme and Chlorophylls. Dailey HA, ed, pp 235-86. Mc Graw-Hill Book Co., New York.
  • Labbe-Bois R, Volland C. (1977) Changes in the activities of the protoheme-synthesizing system during the growth of yeast under different conditions. Arch Biochem Biophys.; 179: 565-77.
  • Labbe-Bois R, Rytka J, Litwińska J, Biliński T. (1977) Analysis of heme biosynthesis in catalase and cytochrome deficient yeast mutants. Mol Gen Genet.; 156: 177-83.
  • Mahlitz E. (2002) Die sauerstoffabhängige Coproporphyrinogen III Oxidase (HemF) aus Escherichia coli. Rekombinante Herstellung, biochemische und biophysikalische Charakterisierung. Der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig. Dissertation.
  • Mendes P. (1993) GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci.; 9: 563-71.
  • Morton-Firth CJ, Bray D. (1998) Predicting temporal fluctuations in an intracellular signalling pathway. J Theor Biol.; 192: 117-28.
  • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res.; 27: 29-34.
  • Pawłowski PH, Zielenkiewicz P. (2004) Biochemical kinetics in changing volumes. Acta Biochim Polon.; 51: 231-43.
  • Poulson R, Polglase WJ. (1975) The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae. J Biol Chem.; 250: 1269-74.
  • Pretlow TP, Sherman F. (1967) Porphyrins and zinc porphyrins in normal and mutant strains of yeast. Biochim Biophys Acta.; 148: 629-44.
  • Rytka J, Biliński T, Labbe-Bois R. (1984) Modified uroporphyrinogen decarboxylase activity in a yeast mutant which mimics porphyria cutanea tarda. Biochem J.; 218: 405-13.
  • Savageau MA, Voit EO. (1982) Power-law approach to modeling biological systems; I. Theory. J Ferment Technol.; 60: 221-8.
  • Schuster S, Dandekar T, Mauch K, Reuss M, Fell DA. (2000) Recent developments in metabolic pathway analysis and their potential implications for biotechnology and medicine. In Technological and Medical Implications of Metabolic Control Analysis. Cornish-Bowden A, Cardenas ML, eds, pp 57-66. Kluwer Academic Publishers, Dordrecht.
  • Senior NM, Brocklehurst K, Cooper JB, Wood SP, Erskine P, Shoolingin-Jordan PM, Thomas PG, Warren MJ. (1996) Comparative studies on the 5-aminolaevulinic acid dehydratases from Pisum sativum, Escherichia coli and Saccharomyces cerevisiae. Biochem J.; 320: 401-12.
  • Shi Z, Ferreira GC. (2004) Probing the active site loop motif of murine ferrochelatase by random mutagenesis. J Biol Chem.; 279: 19977-86.
  • Shoolingin-Jordan PM. (1995) Porphobilinogen deaminase and uroporphyrinogen III synthase: structure, molecular biology, and mechanism. J Bioenerg Biomembr.; 27: 181-96.
  • Siepker LJ, Ford M, de Kock R, Kramer S, (1987) Purification of bovine protoporphyrinogen oxidase: immunological cross-reactivity and structural relationship to ferrochelatase. Biochim Biophys Acta.; 913: 349-58.
  • Tomita M, Hashimoto K, Takahashi K, Shimizu T, Matsuzak Y, Miyosh F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison C. (1999) E-CELL: Software environment for whole cell simulation. Bioinformatics.; 15: 72-84.
  • Tsai SF, Bishop DF, Desnick RJ. (1987) Purification and properties of uroporphyrinogen III synthase from human erythrocytes. J Biol Chem.; 262: 1268-73.
  • Tyson CB, Lord PG, Wheals AE. (1979) Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol.; 138: 92-8.
  • Voit EO, Savageau MA. (1982a) Power-law approach to modeling biological systems; II. Application to ethanol production. J Ferment Technol.; 60: 229-32.
  • Voit EO, Savageau MA. (1982b) Power-law approach to modeling biological systems; III. Methods of analysis. J Ferment Technol.; 60: 233-41.
  • Voit EO, Ferreira AEN. (1998) Buffering in models of integrated biochemical systems. J Theor Biol.; 191: 429-38.
  • Żołąadek T, Nhi NB, Rytka J. (1996) Saccharomyces cerevisiae mutants defective in heme biosynthesis as a tool for studying the mechanism of phototoxicity of porphyrins. Photochem Photobiol.; 64: 957-62.
Document Type
Publication order reference
YADDA identifier
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.